I can't remember if you can drop unconscious bodies into water deep enough for them to sink into without it being an issue. I know there's some water you can't, but that water is also electrified, so it doesn't really work for checking for fish augmentations.
You definitely can't just drop them through a manhole cover and into the sewers and expect them to be okay. Don't ask me how I know that. I certainly never cleared out an area and then dropped everyone into the sewers afterward. That's an absurd accusation and you should apologize for it.